wwpdb
PDB FORMAT Version 2.3
Main Index
HELIX
TURN
SHEET

Secondary Structure Section

The secondary structure section of a PDB file describes helices, sheets, and turns found in protein and polypeptide structures.

HELIX

Overview

HELIX records are used to identify the position of helices in the molecule. Helices are named and numbered. The residues where the helix begins and ends are noted, as well as the total length.

Record Format 

COLUMNS       DATA TYPE        FIELD        DEFINITION
--------------------------------------------------------------------
 1 -  6       Record name      "HELIX "
 8 - 10       Integer          serNum       Serial number of the helix.
                                            This starts at 1 and increases
                                            incrementally.
12 - 14       LString(3)       helixID      Helix identifier. In addition
                                            to a serial number, each helix is
                                            given an alphanumeric character
                                            helix identifier.
16 - 18       Residue name     initResName  Name of the initial residue.
20            Character        initChainID  Chain identifier for the chain
                                            containing this helix.
22 - 25       Integer          initSeqNum   Sequence number of the initial
                                            residue.
26            AChar            initICode    Insertion code of the initial
                                            residue.
28 - 30       Residue name     endResName   Name of the terminal residue of
                                            the helix.
32            Character        endChainID   Chain identifier for the chain
                                            containing this helix.
34 - 37       Integer          endSeqNum    Sequence number of the terminal
                                            residue.
38            AChar            endICode     Insertion code of the terminal
                                            residue.
39 - 40       Integer          helixClass   Helix class (see below).
41 - 70       String           comment      Comment about this helix.
72 - 76       Integer          length       Length of this helix.

Details

  • Additional HELIX records with different serial numbers and identifiers occur if more than one helix is present.
  • The initial residue is the N-terminal residue of the helix.
  • Helices are classified as follows:

    •                 TYPE OF HELIX          CLASS NUMBER 
                                       (COLUMNS 39 - 40)
      ---------------------------------------------------
      Right-handed alpha (default)       1
      Right-handed omega                 2
      Right-handed pi                    3
      Right-handed gamma                 4
      Right-handed 310                   5
      Left-handed alpha                  6
      Left-handed omega                  7
      Left-handed gamma                  8
      27 ribbon/helix                    9
      Polyproline                       10

    Relationships to Other Record Types

    There may be related information in the REMARKs.

    Example 

             1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890123456
HELIX    1  HA GLY A   86  GLY A   94  1                                   9
HELIX    2  HB GLY B   86  GLY B   94  1                                   9

    SHEET

    Overview

    SHEET records are used to identify the position of sheets in the molecule. Sheets are both named and numbered. The residues where the sheet begins and ends are noted.

    Record Format 

    COLUMNS     DATA TYPE        FIELD           DEFINITION
--------------------------------------------------------------
 1 -  6     Record name      "SHEET "
 8 - 10     Integer          strand       Strand number which starts at 1 
                                          for each strand within a sheet 
                                          and increases by one.
12 - 14     LString(3)       sheetID      Sheet identifier.
15 - 16     Integer          numStrands   Number of strands in sheet.
18 - 20     Residue name     initResName  Residue name of initial residue.
22          Character        initChainID  Chain identifier of initial 
                                          residue in strand.
23 - 26     Integer          initSeqNum   Sequence number of initial 
                                          residue in strand.
27          AChar            initICode    Insertion code of initial residue
                                          in strand.
29 - 31     Residue name     endResName   Residue name of terminal residue.
33          Character        endChainID   Chain identifier of terminal
                                          residue.
34 - 37     Integer          endSeqNum    Sequence number of terminal
                                          residue.
38          AChar            endICode     Insertion code of terminal 
                                          residue.
39 - 40     Integer          sense        Sense of strand with respect to
                                          previous strand in the sheet. 0
                                          if first strand, 1 if parallel,
                                          -1 if anti-parallel.
42 - 45     Atom             curAtom      Registration. Atom name in 
                                          current strand.
46 - 48     Residue name     curResName   Registration. Residue name in
                                          current strand.
50          Character        curChainId   Registration. Chain identifier in
                                          current strand.
51 - 54     Integer          curResSeq    Registration. Residue sequence
                                          number in current strand.
55          AChar            curICode     Registration. Insertion code in
                                          current strand.
57 - 60     Atom             prevAtom     Registration. Atom name in
                                          previous strand.
61 - 63     Residue name     prevResName  Registration. Residue name in
                                          previous strand.
65          Character        prevChainId  Registration. Chain identifier in
                                          previous strand.
66 - 69     Integer          prevResSeq   Registration. Residue sequence
                                          number in previous strand.
70          AChar            prevICode    Registration. Insertion code in
                                              previous strand.

    Details

  • The initial residue for a strand is its N-terminus. Strand registration information is provided in columns 39 - 70. Strands are listed starting with one edge of the sheet and continuing to the spatially adjacent strand.
  • The sense in columns 39 - 40 indicates whether strand n is parallel (sense = 1) or anti-parallel (sense = -1) to strand n-1. Sense is equal to zero (0) for the first strand of a sheet.
  • The registration (columns 42 - 70) of strand n to strand n-1 may be specified by one hydrogen bond between each such pair of strands. This is done by providing the hydrogen bonding between the current and previous strands. No registration information should be provided for the first strand.
  • Split strands, or strands with two or more runs of residues from discontinuous parts of the amino acid sequence, are explicitly listed. Provide a description to be included in the REMARK section.

    • Relationships to Other Record Types

    If the entry contains bifurcated sheets or beta-barrels, the relevant REMARK records must be provided. See the REMARK section for details.

    Example 

             1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
SHEET    1   A 5 THR A 107  ARG A 110  0
SHEET    2   A 5 ILE A  96  THR A  99 -1  N  LYS A  98   O  THR A 107
SHEET    3   A 5 ARG A  87  SER A  91 -1  N  LEU A  89   O  TYR A  97
SHEET    4   A 5 TRP A  71  ASP A  75 -1  N  ALA A  74   O  ILE A  88
SHEET    5   A 5 GLY A  52  PHE A  56 -1  N  PHE A  56   O  TRP A  71
SHEET    1   B 5 THR B 107  ARG B 110  0
SHEET    2   B 5 ILE B  96  THR B  99 -1  N  LYS B  98   O  THR B 107
SHEET    3   B 5 ARG B  87  SER B  91 -1  N  LEU B  89   O  TYR B  97
SHEET    4   B 5 TRP B  71  ASP B  75 -1  N  ALA B  74   O  ILE B  88
SHEET    5   B 5 GLY B  52  ILE B  55 -1  N  ASP B  54   O  GLU B  73

    The sheet presented as BS1 below is an eight-stranded beta-barrel. This is represented by a nine- stranded sheet in which the first and last strands are identical. 

    SHEET    1 BS1 9 VAL    13  ILE    17  0                               
SHEET    2 BS1 9 ALA    70  ILE    73  1  O  TRP    72   N  ILE    17  
SHEET    3 BS1 9 LYS   127  PHE   132  1  O  ILE   129   N  ILE    73  
SHEET    4 BS1 9 GLY   221  ASP   225  1  O  GLY   221   N  ILE   130  
SHEET    5 BS1 9 VAL   248  GLU   253  1  O  PHE   249   N  ILE   222  
SHEET    6 BS1 9 LEU   276  ASP   278  1  N  LEU   277   O  GLY   252  
SHEET    7 BS1 9 TYR   310  THR   318  1  O  VAL   317   N  ASP   278  
SHEET    8 BS1 9 VAL   351  TYR   356  1  O  VAL   351   N  THR   318  
SHEET    9 BS1 9 VAL    13  ILE    17  1  N  VAL    14   O  PRO   352

    The sheet structure of this example is bifurcated. In order to represent this feature, two sheets are defined. Strands 2 and 3 of BS7 and BS8 are identical.

    SHEET    1 BS7 3 HIS   662  THR   665  0                               
SHEET    2 BS7 3 LYS   639  LYS   648 -1  N  PHE   643   O  HIS   662  
SHEET    3 BS7 3 ASN   596  VAL   600 -1  N  TYR   598   O  ILE   646  
SHEET    1 BS8 3 ASN   653  TRP   656  0                               
SHEET    2 BS8 3 LYS   639  LYS   648 -1  N  LYS   647   O  THR   655  
SHEET    3 BS8 3 ASN   596  VAL   600 -1  N  TYR   598   O  ILE   646

    TURN

    Overview

    The TURN records identify turns and other short loop turns which normally connect other secondary structure segments.

    Record Format 

    COLUMNS      DATA TYPE        FIELD         DEFINITION
--------------------------------------------------------------------
 1 -  6      Record name      "TURN "
 8 - 10      Integer          seq           Turn number; starts with 1 and
                                            increments by one.
12 - 14      LString(3)       turnId        Turn identifier
16 - 18      Residue name     initResName   Residue name of initial residue in
                                            turn.
20           Character        initChainId   Chain identifier for the chain
                                            containing this turn.
21 - 24      Integer          initSeqNum    Sequence number of initial residue
                                            in turn.
25           AChar            initICode     Insertion code of initial residue 
                                            in turn.
27 - 29      Residue name     endResName    Residue name of terminal residue 
                                            of turn.
31           Character        endChainId    Chain identifier for the chain
                                            containing this turn.
32 - 35      Integer          endSeqNum     Sequence number of terminal 
                                            residue of turn.
36           AChar            endICode      Insertion code of terminal residue
                                            of turn.
41 - 70      String           comment       Associated comment.

    Details

  • Turns include those sets of residues which form beta turns, i.e., have a hydrogen bond linking (C- O)i to (N-H)i +3. Turns which link residue i to i+2 (gamma-bends) may also be included. Others may be also be classified as turns.
  • The initial residue is the N-terminus.

    • Verification/Validation/Value Authority Control

    The validation program checks the number of residues in the given turn. PDB verifies that named residues exist in the ATOM records.

    Relationships to Other Record Types

    There may be related information in the REMARKs.

    Example 

             1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
TURN     1 S1A GLY A  16  GLN A  18     SURFACE                       
TURN     2 FLA ILE A  50  GLY A  52     FLAP                          
TURN     3 S2A ILE A  66  HIS A  69     SURFACE                       
TURN     4 S1B GLY B  16  GLN B  18     SURFACE                       
TURN     5 FLB ILE B  50  GLY B  52     FLAP                          
TURN     6 S2B ILE B  66  HIS B  69     SURFACE

    � 2007 wwPDB